Biomarkers of osteoarthritis

ABSTRACT

Biomarkers, biomarker panels and methods for diagnosing osteoarthritis (OA) and determining treatment are disclosed, using measurement of the expression level of certain polypeptides in a test sample from a subject, including MCP1, IL8, KC, MMP2, MMP3, Apolipoprotein A1, and Apolipoprotein E. Related methods for monitoring OA treatment efficacy, diagnostic reagents, and kits are also described.

REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No.14/175,254, filed Feb. 7, 2014, which is a continuation of U.S. patentapplication Ser. No. 13/041,055, filed Mar. 4, 2011, which claims thebenefit of U.S. Patent Application No. 61/339,511, filed Mar. 5, 2010,the entire contents all of which are herein incorporated by reference.

FIELD OF THE INVENTION

The present disclosure relates to biomarkers of disease and moreparticularly to a plurality of biomarkers, related methods and kits fordiagnosing, staging, and monitoring 10 osteoarthritis.

BACKGROUND

Osteoarthritis (OA) is a debilitating disease that affects human andveterinary, particularly canine patients. Because OA is not typicallydiagnosed early enough to prevent the clinical progression of disease,development of early OA biomarkers has profound ramifications fordiagnostic screening, disease staging, treatment planning andmonitoring. In dogs, certain proteins exhibit differential expressionlevels in synovial fluid when OA is experimentally induced. These aremonocyte chemoattractant protein 1 (MCP1), interleukin 8 (IL8) andkeratinocyte derived chemoattractant (KC), certain Apolipoproteins, andmatrix metalloproteinases (MMPs). It is unknown however whether these orother proteins might be useful as potential biomarkers in spontaneouslyoccurring OA in dogs or in other species including humans. Given thehigh potential value in being able to apply proteomics methods todiagnosis and prognosis of OA disease, and treatment monitoring andelucidation of OA disease mechanisms, it would be useful to identify newOA biomarkers and biomarker combinations with the ability toconveniently and reliably discriminate between individuals in which OAis present and those in which OA is not present, and determine the typeand severity of disease burden.

SUMMARY OF THE INVENTION

In one aspect, the present disclosure provides a method for diagnosing,staging, or monitoring osteoarthritis in a subject comprising: measuringin a biological sample from the subject the level of expression of atleast two polypeptides selected from the group consisting of: MCP1, IL8,KC, MMP2, MMP3, MMP9, IL6, MMP1, RANTES, IL1B, Apolipoprotein A1,Apolipoprotein E, DCN, CILP and COMP, and fragments of any thereof, andany combination thereof, wherein the expression levels of the at leasttwo polypeptides or fragments thereof in the biological sample provide asample protein expression profile indicative of the presence or absence,degree, severity, type or stage of osteoarthritis in the subject. Themethod may further comprise comparing the sample protein expressionprofile to a control protein expression profile, wherein a differencebetween the sample protein expression profile and the control proteinexpression profile is indicative of the presence or absence, degree,severity, type or stage of osteoarthritis in the subject. In the method,the subject can be at risk of having or is suspected of havingosteoarthritis. The level of expression of the at least two polypeptidesin the biological sample can be measured by many methods as detailedfurther herein below, including but not limited to detecting alterationsin DNA due to a process selected from the group consisting of DNAamplification, DNA methylation/demethylation, and single nucleotidepolymorphisms. In another aspect, the present disclosure provides an OAbiomarker expression profile comprising polypeptide expression levelinformation for two or more polypeptides selected from the groupconsisting of: MCP1, IL8, KC, MMP2, MMP3, IL6, MMP1, RANTES, MMP9, IL1B,Apolipoprotein A1, Apolipoprotein E, DCN, CILP and COMP and fragments ofany thereof, and any combination thereof, obtained from a biologicalsample from a subject suspected of having osteoarthritis. An OAexpression profile may further comprise polypeptide expression levelinformation for at least one biological sample obtained from at leastone healthy subject. Biological samples from the subject suspected ofhaving osteoarthritis and the healthy subject or subjects may eachcomprise a sample of synovial fluid, a sample of whole blood, a sampleof blood plasma, a sample of serum, a sample of urine, or a sample ofsaliva. Preferably, the biological samples are samples of synovialfluid. Multiple biological samples of the same or different type may beobtained from each subject, OA expression level information obtainedfrom each sample, and the results combined in a single OA expressionprofile. In another aspect, the present disclosure provides a diagnosticreagent for osteoarthritis comprising two or more antibodies against anytwo or more OA biomarkers or fragments thereof selected from the groupconsisting of: MCP1, IL8, KC, MMP2, MMP3, IL6, MMP1, RANTES, MMP9, IL1B,Apolipoprotein A1, Apolipoprotein E, DCN, CILP and COMP and fragments ofany thereof. The diagnostic reagent may be provided in a kit. In anotheraspect, the present disclosure provides a kit for diagnosingosteoarthritis in a subject, the kit comprising: at least two OAbiomarker detection reagents that each specifically bind to an OApolypeptide selected from the group consisting of MCP1, IL8, KC, MMP2,MMP3, IL6, MMP1, RANTES, MMP9, IL1B, Apolipoprotein A1, ApolipoproteinE, DCN, CILP and COMP and fragments of any thereof, or at least two OAbiomarker detection reagents that each specifically bind to at leastpart of a polynucleotide sequence coding for at least two of the OApolypeptides, wherein the specific binding of the reagent is indicativeof the expression level of at least one OA polypeptide in a biologicalsample from a subject. In the kit, the at least one reagent thatspecifically detects expression of at least one biomarker may comprise anucleic acid probe complementary to at least part of a polynucleotidesequence coding for one of the polypeptides. A nucleic acid probe can bea cDNA or an oligonucleotide. The at least one OA biomarker detectionreagent can be immobilized on a substrate surface. The kit may compriseat least two biomarker detection reagents arranged on the substratesurface.

In the kit, at least two biomarker reagents can be arranged on asubstrate surface to comprise a microarray. In another aspect, thepresent disclosure provides a method for identifying a candidatesubstance as a therapeutic agent for treating osteoarthritis,comprising: a) administering the candidate substance to a subjectdiagnosed with spontaneous osteoarthritis; b) measuring the expressionlevel of two or more OA polypeptides selected from the group consistingof MCP1, IL8, KC, MMP2, MMP3, IL6, MMP1, RANTES, MMP9, IL1B,Apolipoprotein A1, Apolipoprotein E, DCN, CILP and COMP in a biologicalsample from the subject; and c) selecting the candidate substance as acandidate therapeutic agent for treating osteoarthritis if theexpression level of each of the two or more OA polypeptides in thebiological sample is lower than or equal to the expression level for theselected two or more OA polypeptides in a biological sample from acontrol subject not administered the test substance.

In another aspect, the present disclosure provides a method formonitoring the effect of a treatment of osteoarthritis in a subjectcomprising: a) obtaining a first OA biomarker expression profilecomprising measuring the expression level of two or more OA polypeptidesselected from the group consisting of MCP1, IL8, KC, MMP2, MMP3, IL6,MMP1, RANTES, MMP9, IL1B, Apolipoprotein A1, Apolipoprotein E, DCN, CILPand COMP in a first biological sample obtained from the subject beforethe osteoarthritis treatment is administered to the subject; b)obtaining a second OA biomarker expression profile comprising measuringthe expression level of the two or more OA polypeptides selected in (a),in a second biological sample obtained from the subject after or whilethe osteoarthritis treatment is administered to the subject; and c)comparing the first OA biomarker expression profile with the second OAbiomarker expression profile, wherein if the expression level of each ofthe two or more selected OA polypeptides in the first OA biomarkerexpression profile is lower than or equal to the expression level forthe selected two or more OA polypeptides in the second biological samplefrom the subject is indicative of a therapeutic effect of theosteoarthritis treatment in the subject.

In another aspect, the present disclosure provides a method for treatingosteoarthritis in a canine subject comprising: (i) requesting theresults of a first biomarker profile analysis of a test biological fluidsample from the subject and (ii) administering a treatment for OA to thesubject when the results of the biomarker profile analysis areindicative of the presence of OA in the subject, wherein the biomarkerprofile analysis comprises: (a) measuring an expression level of atleast two osteoarthritis marker polypeptides in the test sample using aprotein detection method to determine a first OA biomarker profile,wherein the osteoarthritis marker polypeptides are selected from thegroup consisting of: MCP1, IL8, and KC; (b) measuring an expressionlevel of each osteoarthritis marker polypeptide used in (a) in a controlbiological fluid sample from a control canine subject in which OA is notpresent using the protein detection method used in (a) to determine asecond OA biomarker profile; and (c) comparing the first OA biomarkerprofile from (a) to the second OA biomarker profile from (b) wherein adifference between the first OA biomarker profile and the second OAbiomarker profile is indicative of the presence of osteoarthritis in thesubject. In the method, the level of expression of all three of MCP1,IL8, and KC can be measured. The level of expression of at least oneadditional osteoarthritis marker polypeptide can be measured. The atleast one additional osteoarthritis marker polypeptide can be selectedfor example from the group consisting of MMP2 and MMP3. The method mayinclude for example measuring in the biological fluid samples from thecanine test and control subjects the level of expression of all five ofMCP1, IL8, KC, MMP2 and MMP3. The method may further comprise measuringin the biological fluid samples from the canine test and controlsubjects the level of expression of at least one additionalosteoarthritis marker selected from Apolipoprotein A1 and ApolipoproteinE. The method may include measuring the level of expression of at leastseven osteoarthritis marker polypeptides. The method may further includemonitoring the effect of the treatment of osteoarthritis in the subjectby obtaining the results of a second biomarker profile analysis andcomprising the results to the first biomarker profile analysis. In sucha method, the selected osteoarthritis marker polypeptides may compriseMCP-1, IL8, KC, MMP2, MMP3, Apolipoprotein A1 and Apolipoprotein E. Thesubject may be at risk of having, or is suspected of havingosteoarthritis. The protein detection method used may be selected fromthe group consisting of: LUMINEX, ELISA, immunoassay, mass spectrometry,high performance liquid chromatography, two-dimensional electrophoresis,Western blotting, protein microarray, and antibody microarray. In anexemplary method, the protein detection method is an immunoassay.

In any of the above methods, the biological sample or samples maycomprise any one of synovial fluid, whole blood, blood plasma, serum,urine, and saliva. In an exemplary method, the biological sample(s)comprise synovial fluid. Preferably, the level of expression of at leastfour polypeptides is measured. In any of the methods, the subject may bea mammal. Preferably the subject is a human or a canine. In an exemplaryembodiment of any of the above methods, the subject is a canine and themethod may comprise measuring in a biological sample from the subjectthe level of expression of MCP1, IL8, KC, MMP2 and MMP3, or fragmentsthereof. In another exemplary embodiment of any of the above methods,the subject is a human and the method may comprise measuring in abiological sample from the subject the level of expression of MCP1, IL6,IL8, KC and MMP1, or fragments thereof. Such a method may furthercomprise measuring in the biological sample the level of expression ofRANTES, or fragments thereof. In any of the above methods, theexpression level of each of the at least two polypeptides in thebiological sample from the subject is measured using a method selectedfrom the group consisting of: LUMINEX, ELISA, immunoassay, massspectrometry, high performance liquid chromatography, two-dimensionalelectrophoresis, qPCR, RT-PCR, nucleic acid microarray, in situhybridization, SAGE, Western blotting, protein microarray, and antibodymicroarray.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A is a bar graph showing levels (Mean±SE concentrations (pg/ml)),of Cartilage Intermediate Layer Protein (CILP), Decorin and COMP in dogswith subclinical OA and in dogs with clinical OA following removal ofhigh abundance proteins.

FIG. 1B is a bar graph showing levels (Mean±SE concentrations (pg/ml)),of Apolipoprotein A1 and Apolipoprotein E in dogs with subclinical OAand in dogs with clinical OA following removal of high abundanceproteins.

FIG. 2A is a bar graph showing levels (Mean±SE concentrations (pg/ml)),of IL8, KC, MCP1 and MMP3 in normal dogs and in dogs with spontaneousknee OA before and after 10 surgery.

FIG. 2B is a bar graph showing levels (Mean±SE concentrations (pg/ml)),of MMP2 in normal dogs and in dogs with spontaneous knee OA before andafter surgery.

FIG. 3 is a set of bar graphs summarizing (Mean±SE) MMP/cytokine log(pg/ml) levels in synovial fluid samples from normal patients and frompatients with OA immediately preceding a total knee arthroplastyprocedure.

DETAILED DESCRIPTION OF THE INVENTION A. Definitions

Section headings as used in this section and the entire disclosureherein are not intended to be limiting.

As used herein, the singular forms “a,” “an” and “the” include pluralreferents unless the context clearly dictates otherwise. For therecitation of numeric ranges herein, each intervening number therebetween with the same degree of precision is explicitly contemplated.For example, for the range 6-9, the numbers 7 and 8 are contemplated inaddition to 6 and 9, and for the range 6.0-7.0, the numbers 6.0, 6.1,6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9 and 7.0 are explicitly 25contemplated.

a) Antibody

As used herein, the term “antibody” refers to a protein consisting ofone or more polypeptides substantially encoded by immunoglobulin genesor fragments of immunoglobulin genes, and encompasses polyclonalantibodies, monoclonal antibodies, and fragments thereof, as 5 well asmolecules engineered from immunoglobulin gene sequences. The recognizedimmunoglobulin genes include the kappa, lambda, alpha, gamma, delta,epsilon and mu constant region genes, as well as myriad immunoglobulinvariable region genes. Light chains are classified as either kappa orlambda. Heavy chains are classified as gamma, mu, alpha, delta, orepsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA,IgD and IgE, 10 respectively.

b) Detectable Label

As used herein the term “detectable label” refers to any moiety thatgenerates a measurable signal via optical, electrical, or other physicalindication of a change of state of a molecule or molecules coupled tothe moiety. Such physical indicators encompass spectroscopic,photochemical, biochemical, immunochemical, electromagnetic,radiochemical, and chemical means, such as but not limited tofluorescence, chemifluorescence, chemiluminescence, and the like.

c) Marker

The terms “marker” or “biomarker” as used interchangeably herein referto any molecule used as a target for analyzing test samples obtainedfrom subjects, and encompass proteins or polypeptides themselves as wellas antibodies against same that may be present in a test sample.Proteins or polypeptides used as a marker include any variants andfragments thereof, and in particular, immunologically detectablefragments. For example, it is appreciated that variants of a markerpolypeptide are encoded by the same gene, but can differ in theirisoelectric point or molecular weight or both as a result of alternativeprocessing such as alternative splicing and/or differences inpost-translational modification (e.g., glycosylation, acylation, and/orphosphorylation). It will further be appreciated that cellular proteinscan be damaged as a result of a disease process such as inflammation andmay fragment and thus that proteins or polypeptides used as a markeraccording to the present disclosure include fragments thereof.Additionally it will be recognized that certain markers can besynthesized in an inactive form that is subsequently converted to anactive form by proteolysis. Proteins or fragments thereof can also occuras part of a complex. Proteins or polypeptides used as markers accordingto the present disclosure also include such complexes. The terms“biomarker” and “marker” also encompass nucleic acid moleculescomprising a nucleotide sequence that codes for a marker protein, andalso polynucleotides that can hybridize under stringent conditions witha part of such nucleic acid molecules. An “OA biomarker” and “OA marker”as used interchangeably herein, refer to a protein, polypeptide,antibodies against same and any fragment thereof, that may be present ina test sample from a subject, and has an expression level that has beenfound to be indicative of the presence of OA in the subject as describedherein, and these terms also encompass any nucleic acid moleculecomprising a nucleotide sequence that codes for an OA marker protein.

d) Subject

As used herein, the terms “subject” and “patient” are usedinterchangeably irrespective of whether the subject has or is currentlyundergoing any form of treatment. As used herein, the terms “subject”and “subjects” refer to any vertebrate, including, but not limited to, amammal (e.g., cow, pig, camel, llama, horse, goat, rabbit, sheep,hamsters, guinea pig, cat, dog, rat, and mouse, a non-human primate (forexample, a monkey, such as a cynomolgous monkey, chimpanzee, etc) and ahuman). Preferably, the subject is a canine or a human.

e) Test Sample

As used herein, the term “test sample” generally refers to a biologicalmaterial being tested for and/or suspected of containing an analyte ofinterest. The biological material may be derived from any biologicalsource but preferably is a biological fluid likely to contain theanalyte of interest. Examples of biological materials include, but arenot limited to, stool, whole blood, serum, plasma, red blood cells,platelets, interstitial fluid, saliva, ocular lens fluid, cerebralspinal fluid, sweat, urine, ascites fluid, mucous, nasal fluid, sputum,synovial fluid, peritoneal fluid, vaginal fluid, menses, amniotic fluid,semen, soil, etc. Preferably, the test sample is a synovial fluidsample.

The test sample may be used directly as obtained from the biologicalsource or following a pretreatment to modify the character of thesample. For example, such pretreatment may include preparing plasma fromblood, diluting viscous fluids and so forth. Methods of pretreatment mayalso involve filtration, precipitation, dilution, distillation, mixing,concentration, inactivation of interfering components, the addition ofreagents, lysing, etc. If such methods of pretreatment are employed withrespect to the test sample, such pretreatment methods are such that theanalyte of interest remains in the test sample at a concentrationproportional to that in an untreated test sample (e.g., namely, a testsample that is not subjected to any such pretreatment method(s)).

f) Osteoarthritis

As used herein, the term “osteoarthritis” (abbreviated as “OA”), refersto the disease also known as osteoarthrosis and degenerative jointdisease, characterized by inflammation and damage to, or loss ofcartilage in any joint or joints, and joint pain. Clinical standards fordiagnosing osteoarthritis in subjects including mammalian subjects suchas canines and humans are well known and include for example swelling orenlargement of joints, joint tenderness or pain, decreased range ofmotion in joints, visible joint deformities such as bony growths, andcrepitus. Symptoms can be identified by clinical observation andhistory, or imaging including MRI and X-ray. Criteria for diagnosing thepresence or absence of OA and severity or degree of OA include but arenot limited to the ACR Criteria for knee OA (R. Altman et al.,Development of criteria for the classification and reporting ofosteoarthritis: Classification of osteoarthritis of the knee: Diagnosticand Therapeutic Criteria Committee of the American RheumatismAssociation. ARTHRITIS RHEUM. August 29(8):1039-1049(1986)), functionalstatus criteria according to WOMAC (N. Bellamy et al., 1988, Validationstudy of WOMAC: a health status instrument for measuring clinicallyimportant patient relevant outcomes to antirheumatic drug therapy inpatients with osteoarthritis of the hip or knee. J RHEUMATOL15:1833-1840), and radiological standards for evaluating OA diseaseseverity according to the Kellgren and Lawrence method for knee OA(Kellgren, J. H. and J. S. Lawrence, Radiological assessment ofosteo-arthrosis. ANN RHEUM DIS 16:494-502).

g) Expression

The term “expression,” as used herein, refers to the conversion of theDNA sequence information into messenger RNA (mRNA) or protein.Expression may be monitored by measuring the levels of full-length mRNA,mRNA fragments, full-length protein, or protein fragments. Expressionmay also be inferred by assessing alterations in the DNA relative to acontrol state. Alterations in DNA that affect expression includeamplification (increased copy number) of the DNA, changes in themethlyation status of the regulatory region of a gene, or singlenucleotide polymorphisms in the regulatory region of a gene.

h) Hybridization

The term “hybridization,” as used herein, refers to the process ofannealing or base-pairing via specific hydrogen bonds between twocomplementary single-stranded nucleic acids. The “stringency ofhybridization” is determined by the conditions of temperature and ionicstrength. Nucleic acid hybrid stability is expressed as the meltingtemperature or Tm, which is the temperature at which the hybrid is 50%denatured under defined conditions. Equations have been derived toestimate the Tm of a given hybrid; the equations take into account theG+C content of the nucleic acid, the length of the hybridization probe,etc. (e.g., Sambrook et al, 1989, chapter 9). To maximize the rate ofannealing of the probe with its target, hybridizations are generallycarried out in solutions of high ionic strength (6×SSC or 6×SSPE) at atemperature that is about 20-25° C. below the Tm. If the sequences to behybridized are not identical, then the hybridization temperature isreduced 1-1.5° C. for every 1% of mismatch. In general, the washingconditions are as stringent as possible (i.e., low ionic strength at atemperature about 12-20° C. below the calculated Tm). As an example,highly stringent conditions typically involve hybridizing at 68° C. in6×SSC/5×Denhardt's solution/1.0% SDS and washing in 0.2×SSC/0.1% SDS at65° C. The optimal hybridization conditions generally differ betweenhybridizations performed in solution and hybridizations usingimmobilized nucleic acids. One skilled in the art will appreciate whichparameters to manipulate to optimize hybridization.

i) Nucleic Acid Molecule

The term “nucleic acid molecule” and “polynucleotide” as usedinterchangeably herein, refer to sequences of linked nucleotides. Thenucleotides may be deoxyribonucleotides or ribonucleotides, they may bestandard or non-standard nucleotides; they may be modified orderivatized nucleotides; they may be synthetic analogs. The nucleotidesmay be linked by phosphodiester bonds or non-hydrolyzable bonds. Thenucleic acid may comprise a few nucleotides (i.e., oligonucleotide), orit may comprise many nucleotides (i.e., polynucleotide). The nucleicacid may be single-stranded or double-stranded.

j) Protein and Protein Fragment

The terms “protein”, “polypeptide”, and “peptide” as interchangeablyherein, refer to molecules composed of multiple amino acids havingsequences of a variety of lengths acid including the full-length nativeprotein or a shorter fragment of the full-length protein. These may bein neutral forms or as salts, either unmodified or modified by processesincluding glycosylation, side chain oxidation, and phosphorylation, orby the addition of other moieties attached to amino acid side chains,including but not limited to glycosyl units, lipids, and inorganic ionssuch as phosphates. Modifications may also include chemical conversionof amino acid side chains, such as oxidation of sulfhydryl groups.Molecules with such modifications are encompassed by the terms, providedthat the modification(s) do not change its specific properties. Itshould understood that the term “protein”, and its equivalents as usedherein, encompasses protein isoforms encoded by the same gene that maydiffer in pI, MW, or both. Such isoforms may have different amino acidsequences resulting, for example, from differential processing such asalternative splicing, or post-translational modification(s). The term“protein fragment”, as used herein, refers to a polypeptide comprisingan amino acid sequence of at least 5 amino acid residues (preferably, atleast 10 amino acid residues, at least 15 amino acid residues, at least20 amino acid residues, at least 25 amino acid residues, at least 40amino acid residues, at least 50 amino acid residues, at least 60 aminoacid residues, at least 70 amino acid residues, at least 80 amino acidresidues, at least 90 amino acid residues, at least 100 amino acidresidues, at least 125 amino acid residues, at least 150 amino acidresidues, at least 175 amino acid residues, at least 200 amino acidresidues, or at least 250 amino acid residues) of the amino acidsequence of a second polypeptide. The fragment of a marker protein mayor may not possess a functional activity of the full-length nativeprotein.

B. Osteoarthritis Biomarkers and Arrays

The methods described herein, and diagnostic reagents, kits and relatedinventions disclosed herein are based in part on the surprisingdiscovery of a plurality of molecular markers, the expression levels ofwhich consistently differentiate between healthy subjects and subjectswith OA. The same plurality of markers is able to distinguish betweenpre- and post-surgical OA subjects, thus also indicating that OAtreatment efficacy can be evaluated with these markers. The molecularmarkers are genes whose altered expression in subject, as measured froma readily obtained biological sample from the subject, is indicative ofthe presence of OA in the subject. Also provided herein are methods ofusing the molecular markers to identify a candidate substance as atherapeutic substance for OA treatment, methods for determining OAtreatment efficacy in a subject, and OA diagnostic reagents and kits.

As used herein, an “OA biomarker” is indicative of OA when theexpression level or quantity or structure of the biomarker is foundsignificantly more often in subjects with OA present, or having OA ofthe same degree, severity, type or stage, than in subjects without OA,or lacing OA of the same degree, severity, type or stage. Significanceof an expression level, quantity or structure of the OA marker, ascompared to a control, is determined using routine statistical methodsby applying accepted confidence levels, e.g. at a minimum of 95%. Itwill be understood, for example, that cut-off or threshold expressionlevels for each OA biomarker may set according to many factors includingthe degree of correlation of expression level with clinical orsubclinical OA indicators. For example, an expression level of abiomarker that is indicative of OA can be, for example, that found in atleast 60% of patients who have the disease and is found in less than 10%of subjects who do not have the disease. More preferably, an expressionlevel is indicative of OA if found in at least 70%, at least 75%, atleast 80%, at least 85%, at least 90%, at least 95%, at least 97%, atleast 98%, at least 99% or more in subjects who have the disease and isfound in less than 20%, less than 10%, less than 8%, less than 5%, lessthan 2.5%, or less than 1% of subjects who do not have the disease.

An “OA expression profile” is any physical representation of theexpression levels of a set of two or more selected OA markers, asdetermined from one or more biological samples from one or more subjectsknown to have OA, known to have OA of a particular type (subtype I orsubtype II), known to have OA of a particular stage (early or late), orknown to be free of OA. A profile for a particular subject or group ofsubjects may include expression level information from multiple types ofbiological samples that have been analyzed separately for OA markerexpression levels. For example, an OA expression profile for a subjectmay include OA marker expression level information from a urine sampleand a blood sample from the subject, and the results combined in asingle profile representing the OA marker expression levels from bothsamples. A single expression profile may include expression levelinformation from any two or more biological samples selected fromsynovial fluid, whole blood, blood plasma, serum, urine, and saliva, anda complete profile may include expression level information from anythree or four biological samples selected from synovial fluid, urine,saliva, and whole blood, blood plasma or serum.

One skilled in the art will appreciate that the more samples from asubject that are examined, the more reliable the determination of thepresence or absence, degree, severity, type or stage of OA in thesubject. The profile may be represented in visual graphical form, forexample on paper or on a computer display; in a three dimensional formsuch as an array; and/or stored in a computer-readable medium. Anexpression profile may correspond to a particular status of OA (e.g.,presence or absence of OA disease, severity (clinical or subclinical)),type (subtype I or subtype II OA), degree (degree of cartilage damage)or stage (early OA or late OA), and thus provides a template forcomparison to a patient sample. Control profiles can be obtained byanalyzing a biological sample from at least one normal/healthy subject,or multiple samples obtained from a group of normal/healthy subjects, orfrom one or more subjects identified as having comparable OA disease interms of severity, type or stage. Similarly, comparable profiles can beobtained for age-, sex- and body mass index-matched subjects.

The terms “normal” and “healthy” are used herein interchangeably torefer to a subject or subjects who do not display and have no history ofOA symptoms such as joint pain, inflammation, or decrease in function,and have not been diagnosed with OA. A “normal” or “healthy” samplerefers to a sample or samples obtained from a normal/healthy subject. Asubject suspected of having OA″ is a subject that exhibits one or moresymptoms indicative of the presence of OA in the subject, such as butnot limited to joint pain, joint swelling, and crepitus, or a subjectthat may be at risk of, or simply being screened for the presence of OA.Risk factors for developing OA are generally well known and include, forexample, age, overweight or obesity, traumatic injury, breed, and/orfamily history.

An OA biomarker expression profile may for example comprise polypeptideexpression level information for two or more polypeptides selected fromthe group consisting of: MCP1, IL8, KC, MMP2, MMP3, IL6, MMP1, RANTES,MMP9, Apolipoprotein A1, Apolipoprotein E and fragments of any thereof,and any combination thereof, obtained from a biological sample from asubject suspected of having osteoarthritis. More specifically, byanalyzing samples of synovial fluid obtained from healthy patients andfrom patients with early OA or late OA, it has been discovered that thepolypeptides listed in Table 1 discriminate between normal subjects andsubjects with OA. Changes in the expression levels of these marker genesin a subject, as measured in a biological sample from subject, thus maybe used to indicate the presence or absence, degree, severity, type orstage of OA on the subject. The panel of markers (see Table 1) comprisesMCP1, IL8, KC, MMP2, MMP3, IL6, MMP1, RANTES, MMP9, 1L1B, ApolipoproteinA1, Apolipoprotein E, DCN, CILP and COMP. These proteins are found to beup-regulated in synovial fluid samples of subjects with earlyosteoarthritis compared to synovial fluid samples of normal individuals.

For example, altered expression levels of any one or more, preferablytwo or more of the OA markers described herein may be used to determinethe presence or absence, degree, severity, type or stage of OA in one ormore subjects. Altered expression of any 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12 or more of the molecular markers may be used to determine thepresence or absence, degree, severity, type or stage of OA in one ormore subjects. One skilled in the art will appreciate that, generally,the more markers examined, the more accurate the determination of thepresence or absence, degree, severity, type or stage of OA in the one ormore subjects.

TABLE 1 OA Markers Official Name Gene Name GenBank Accession NumberMonocyte Chemoattractant CCL2 Human G: NM_002982 Protein-1 (MCP-1/CCL2)Human P: NP_002973 Canine G: NM_001003297 Canine P: NP_001003297.1Interleukin-8 IL8 Human G: NM_00584 Human P: NP_00575 Canine G:NM_001003200 Canine P: NP_001003200 Keratinocyte CXCL1 Human G:NM_001511 Chemoattractant/ Human P: NP_001502 GRO-alpha (CXCL1) CanineG: Canine P: Matrix Metalloproteinase-2 MMP2 Human G: NM_004530 Human P:NP_004521 Canine G: XM_535300 Canine P: XP_535300 MatrixMetalloproteinase-3 MMP3 Human G: NM_002422 Human P: NP_002413 Canine G:NM_001002967 Canine P: NP_001002967 Interleukin-6 IL6 Human G: NM_000600Human P: NP_000591 Canine G: XM_850499 Canine P: XP_855592 MatrixMetalloproteinase-1 MMP1 Human G: NM_002421 Human P: NP_002412 Canine G:XM_546546 Canine P: XP_546546 RANTES, Chemokine (C-C CCL5 Human G:NM_002985 motif) ligand 5 (CCL5 Human P: NP_002976 Canine G:NM_001003010 Canine P: NP_001003010 Matrix Metalloproteinase-9 MMP9Human G: NM_004994 Human P: NP_004985 Canine G: NM_001003219 Canine P:NP_001003219 Interleukin-1β IL1B Human G: NM_000576 Human P: NP_000567Canine G: NM_001037971 Canine P: NP_001033060 Apolipoprotein A1 APOA1Human G: NM_000039 Human P: NP_000030 Canine G: NM_001197048 Canine P:XP_536564 Apolipoprotein E APOE Human G: NM_000041 Human P: NP_000032Canine G: XM_533644 Canine P: XP_533644 Decorin DCN Human G: NM_001920Human P: NP_001911 Canine G: NM_001003228 Canine P: NP_001003228Cartilage Intermediate CILP Human G: NM_003613 Layer Protein Human P:NP_003604 Canine G: XM_544728 Canine P: XP_544728 Cartilage oligomericmatrix COMP Human G: NM_000095 Protein Human P: NP_000086 Canine G:XM_860228 Canine P: XP_865321

Measuring the expression of any OA markers or a plurality of the OAmarkers may be accomplished by a variety of techniques that are wellknown in the art. Expression may be monitored directly by detectingproducts of the OA marker genes (i.e., mRNA or protein), or it may beassessed indirectly by detecting alterations in the DNA (e.g.,amplification, methylation, etc.) that affect expression of the OAmarker genes. RNA, protein, or DNA may be isolated from cells ofinterest using techniques well known in the art and disclosed instandard molecular biology reference books, such as Ausubel et al.,(2003) CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, NewYork, N.Y.

Detection of the RNA products of the OA marker genes may be accomplishedby a variety of methods. Some methods are quantitative and allowestimation of the original levels of RNA between the OA sample andcontrol sample, whereas other methods are merely qualitative. Additionalinformation regarding the methods presented below may be found forexample in Ausubel et al., (2003) CURRENT PROTOCOLS IN MOLECULARBIOLOGY, John Wiley & Sons, New York, N.Y., or Sambrook et al. (1989)MOLECULAR CLONING: A LABORATORY MANUAL, Cold Spring Harbor Press, ColdSpring Harbor, N.Y. A person skilled in the art will know whichparameters may be manipulated to optimize detection of the mRNA ofinterest.

Quantitative real-time PCR (QRT-PCR) may be used to measure thedifferential expression of any OA marker in an OA sample and controlsample. In QRT-PCR, the RNA template is generally reverse transcribedinto cDNA, which is then amplified via a PCR reaction. The PCRamplification process is catalyzed by a thermostable DNA polymerase.Non-limiting examples of suitable thermostable DNA polymerases includeTaq DNA polymerase, Pfu DNA polymerase, Tli (also known as Vent) DNApolymerase, Tfl DNA polymerase, and Tth DNA polymerase. The PCR processmay comprise three steps (i.e., denaturation, annealing, and extension)or two steps (i.e., denaturation and annealing/extension). Thetemperature of the annealing or annealing/extension step can and willvary, depending upon the amplification primers. That is, theirnucleotide sequences, melting temperatures, and/or concentrations. Thetemperature of the annealing or annealing/extending step may range fromabout 50° C. to about 75° C. The amount of PCR product is followedcycle-by-cycle in real time, which allows for determination of theinitial concentrations of mRNA. The reaction may be performed in thepresence of a dye that binds to double-stranded DNA, such as SYBR Green.The reaction may also be performed with fluorescent reporter probes,such as TAQMAN® probes (Applied Biosystems, Foster City, Calif.) thatfluoresce when the quencher is removed during the PCR extension cycle.Fluorescence values are recorded during each cycle and represent theamount of product amplified to that point in the amplification reaction.The cycle when the fluorescent signal is first recorded as statisticallysignificant is the threshold cycle (Ct). To minimize errors and reduceany sample-to-sample variation, QRT-PCR is typically performed using aninternal standard. The ideal internal standard is expressed at aconstant level among different tissues, and is unaffected by theexperimental treatment. Suitable internal standards include, but are notlimited to, mRNAs for the housekeeping genesglyceraldehyde-3-phosphate-dehydrogenase (GAPDH) and beta-actin.

Reverse-transcriptase PCR (RT-PCR) may also be used to measure thedifferential expression of an OA marker. As described above, the RNAtemplate is reverse transcribed into cDNA, which is then amplified via atypical PCR reaction. After a set number of cycles the amplified DNAproducts are typically separated by gel electrophoresis. Comparison ofthe relative amount of PCR product amplified in the different cells willreveal whether the molecular marker is differentially expressed in an OAsample.

Differential expression of an OA marker may also be measured using anucleic acid microarray. In this method, single-stranded nucleic acids(e.g., cDNAs, oligonucleotides, etc.) are plated, or arrayed, on a solidsupport. The solid support may be a material such as glass,silica-based, silicon-based, a synthetic polymer, a biological polymer,a copolymer, a metal, or a membrane. The form or shape of the solidsupport may vary, depending on the application. Suitable examplesinclude, but are not limited to, slides, strips, plates, wells,microparticles, fibers (such as optical fibers), gels, and combinationsthereof. The arrayed immobilized sequences are generally hybridized withspecific DNA probes from the cells of interest. Fluorescently labeledcDNA probes may be generated through incorporation of fluorescentlylabeled deoxynucleotides by reverse transcription of RNA extracted fromthe cells of interest. The probes are hybridized to the immobilizednucleic acids on the microchip under highly stringent conditions. Afterstringent washing to remove non-specifically bound probes, the chip isscanned by confocal laser microscopy or by another detection method,such as a CCD camera. Quantitation of hybridization of each arrayedelement allows for assessment of corresponding mRNA abundance. With dualcolor fluorescence, separately labeled cDNA probes generated from twosources of RNA are hybridized pairwise to the array. The relativeabundance of the transcripts from the two sources corresponding to eachspecified molecular marker is thus determined simultaneously. Microarrayanalysis may be performed by commercially available equipment, followingmanufacturer's protocols, such as by using the Affymetrix GenChiptechnology, or Incyte's microarray technology.

Differential expression of an OA marker may also be measured usingNorthern blotting. For this, RNA samples are first separated by size viaelectrophoresis in an agarose gel under denaturing conditions. The RNAis then transferred to a membrane, crosslinked, and hybridized, underhighly stringent conditions, to a labeled DNA probe. After washing toremove the non-specifically bound probe, the hybridized labeled speciesare detected using techniques well known in the art. The probe may belabeled with a radioactive element, a chemical that fluoresce whenexposed to ultraviolet light, a tag that is detected with an antibody,or an enzyme that catalyses the formation of a colored or a fluorescentproduct. A comparison of the relative amounts of RNA detected in acontrol sample and a test sample will reveal whether the expression ofthe OA marker or OA markers is changed in the test sample.

Nuclease protection assays may also be used to monitor the differentialexpression of an OA marker in an OA sample and control sample. Innuclease protection assays, an antisense probe hybridizes in solution toan RNA sample. The antisense probe may be labeled with an isotope, afluorophore, an enzyme, or another tag. Following hybridization,nucleases are added to degrade the single-stranded, unhybridized probeand RNA. An acrylamide gel is used to separate the remaining protecteddouble-stranded fragments, which are then detected using techniques wellknown in the art. Again, qualitative differences in expression may bedetected.

Differential expression of an OA marker may also be measured using insitu hybridization. This type of hybridization uses a labeled antisenseprobe to localize a particular mRNA in cells of a tissue section. Thehybridization and washing steps are generally performed under highlystringent conditions. The probe may be labeled with a fluorophore or asmall tag (such as biotin or digoxigenin) that may be detected byanother protein or antibody, such that the labeled hybrid may bevisualized under a microscope. The transcripts of an OA marker may belocalized to the nucleus, the cytoplasm, or the plasma membrane of acell.

Detection of the protein products of the OA markers may be accomplishedby several different techniques, many of which are antibody-based.Additional information regarding the methods discussed below may befound in Ausubel et al., (2003) CURRENT PROTOCOLS IN MOLECULAR BIOLOGY,John Wiley & Sons, New York, N.Y., or Sambrook et al. (1989) MOLECULARCLONING: A LABORATORY MANUAL, Cold Spring Harbor Press, Cold SpringHarbor, N.Y. One skilled in the art will know which parameters may bemanipulated to optimize detection of the protein of interest.

An enzyme-linked immunosorbent assay (ELISA) may be used to detect andquantify protein levels. This method comprises preparing the antigen(i.e., protein of interest), coating the wells of a microtiter platewith the antigen, incubating with an antibody that recognizes theantigen, washing away the unbound antibody, and detecting theantibody-antigen complex. The antibody is generally conjugated to anenzyme, such as horseradish peroxidase or alkaline phosphatase, whichgenerate colorimetric, fluorescent, or chemiluminescent products. AnELISA may also use two antibodies, one of which is specific to theprotein of interest and the other of which recognizes the first antibodyand is coupled to an enzyme for detection. Further, instead of coatingthe well with the antigen, the antibody may be coated on the well. Inthis case, a second antibody conjugated to a detectable compound isadded following the addition of the antigen of interest to the coatedwell.

The Luminex platform (available from Luminex Corp., Austin, Tex.) can beused to detect and quantify protein levels using multiplexed assaysbased on a capture bead system in which microsphere beads arecolor-coded with dyes into up to one hundred distinct sets. Eachcolor-coded bead set is coated with a specific binding reagent such asan antibody specific to a selected protein marker, allowing the captureand detection of specific protein analytes from a very small amount,e.g. a drop of fluid, from a biological sample such as plasma, serum,lysates or synovial fluid. Depending upon which analyte(s) are beingscreened, at least one or several bead sets may be incubated with thesample in order to capture the analytes. A Luminex compact analyzer useslasers to excite the internal dyes that identify each microsphere beads,and also any reporter dye captured during the assay. Multiple readingscan be made on each bead set. Because of the special dye ratioincorporated each bead, each unique bead population can be analyzedseparately after acquisition. An exemplary multiplex immunoassayplatform is also the xMAP platform available from Qiagen Inc.

Relative protein levels may also be measured by Western blotting.Western blotting generally comprises preparing protein samples, usinggel electrophoresis to separate the denatured proteins by mass, andprobing the blot with antibodies specific to the protein of interest.Detection is usually accomplished using two antibodies, the second ofwhich is conjugated to an enzyme for detection or another reportermolecule. Methods used to detect differences in protein levels includecolorimetric detection, chemiluminescent detection, fluorescentdetection, and radioactive detection.

Measurement of protein levels may also be performed using a proteinmicroarray or an antibody microarray. In these methods, the proteins orantibodies are covalently attached to the surface of the microarray orbiochip. The protein of interest is detected by interaction with anantibody, and the antibody/antigen complexes are generally detected viafluorescent tags on the antibody.

Relative protein levels may also be assessed by immunohistochemistry, inwhich a protein is localized in cells of a tissue section by itsinteraction with a specific antibody. The antigen/antibody complex maybe visualized by a variety of methods. One or two antibodies may beused, as described above for ELISA. The detection antibody may be taggedwith a fluorophore, or it may be conjugated to an enzyme that catalyzesthe production of a detectable product. The labeled complex is typicallyvisualized under a microscope.

Changes in the expression of any one or more OA markers may also beassessed by detecting alterations in the DNA encoding each OA markergene. The DNA may be amplified, which is a process whereby the number ofcopies of a region of DNA or a gene is increased. Usually, the amount ofRNA product is also increased, in proportion to the number of additionalcopies of DNA. Amplification of DNA may be detected by PCR techniques,which are well known in the art. Amplification of DNA may also bedetected by Southern blotting, in which genomic DNA is hybridized tolabeled probes under highly stringent conditions, and the labeledhybrids may be detected as described above for Northern blotting.

Changes in the methylation status of DNA may also indicate changes inexpression of any OA marker. The regulatory region of a gene may bemethylated, which entails the addition of a methyl group to the 5-carbonof cytosine in a CpG dinucleotide. Genes that are transcriptionallysilent tend to have methylated or hypermethylated regulatory regions.Thus, demethylation of an OA marker gene may lead to increasedexpression in tissue or cells, which is detectable from a biologicalsample obtained from a subject. Likewise, methylation of an OA markergene may lead to decreased expression in issue or cells, which isdetectable from a biological sample obtained from a subject. Changes inthe methylation status of an OA marker gene in a sample or samples fromone or more subjects with OA, relative to a sample or samples from oneor more control subjects, may be assessed using methylation-sensitiverestriction enzymes to digest DNA followed by Southern detection or PCRamplification. Changes in the methylation status of an OA marker mayalso be detected using a bisulfite reaction based method. For this,sodium bisulfite is used to convert unmethylated cytosines to uracils,and then the methylated cytosines are detected by methylation specificPCR (MSP).

Single nucleotide polymorphisms (SNPs) in the regulatory region of an OAmarker gene may also affect its level of expression. For example, analtered nucleotide may affect the binding of a transcription factor suchthat transcription is up-regulated or down-regulated. The presence of aparticular SNP may be detected by DNA sequencing. A SNP may also bedetected by selective hybridization to an oligonucleotide probe (i. e.,it hybridizes to a sequence containing a particular SNP, but not tosequences without the SNP). A particular SNP may also be detected usinga PCR based technique or an oligonucleotide microarray based assay.

Expression of any one or more of the OA markers can be measured in an OAsample relative to a control sample. The OA cell may be isolated from asubject known to have OA based on generally accepted clinicalindicators, and expression of any OA marker may be examined in vitro.The type of biopsy used to isolated cells can and will vary, dependingupon the location and nature of the OA. A sample of cells, tissue, orbiological fluid such as synovial fluid, may be removed by needleaspiration biopsy. For this, a fine needle attached to a syringe isinserted through the skin and into the organ, tissue or joint capsule ofinterest. The needle may be guided to the region of interest usingultrasound or computed tomography (CT) imaging. Once the needle isinserted into the tissue, a vacuum is created with the syringe such thatcells or fluid may be sucked through the needle and collected in thesyringe. A sample of cells or tissue may also be removed by incisionalor core biopsy. For this, a cone, a cylinder, or a tiny bit of tissue isremoved from the region of interest. This type of biopsy is generallyguided by CT imaging, ultrasound, or an endoscope.

RNA, protein, or DNA may be extracted from any biological samplecontaining cells or tissue, to permit analysis of the expression levelor levels of any one or more OA markers using methods described hereinabove. Biopsied cells or tissue may also be embedded in plastic orparaffin, from which nucleic acids may be isolated. The expression of anOA marker may also be performed in the biopsied cells or tissue in situ(e.g., in situ hybridization, immunohistochemistry).

Expression of an OA marker may also be examined in vivo in a subject. Aparticular mRNA or protein may be labeled with fluorescent dye, abioluminescent marker, a fluorescent semiconductor nanocrystal, or ashort-lived radioisotope, and then the subject may be imaged or scannedusing a variety of techniques, depending upon the type of label.

C. Methods

A method for diagnosing, staging, or monitoring osteoarthritis caninclude, for example, measuring in a biological sample from the subjectthe level of expression of at least two polypeptides selected from thegroup consisting of: MCP1, IL8, KC, MMP2, MMP3, MMP9, IL6, MMP1, RANTES,IL1B, Apolipoprotein A1, Apolipoprotein E, DCN, CILP and COMP, andfragments of any thereof, and any combination thereof, wherein theexpression levels of the at least two polypeptides or fragments thereofin the biological sample provide a sample protein expression profileindicative of the presence or absence, degree, severity, type or stageof osteoarthritis in the subject. The level of expression of the atleast two polypeptides is measured using any of the above protein ornucleic acid quantification techniques, including but not limited to bydetecting alterations in DNA due to a process selected from the groupconsisting of DNA amplification, DNA methylation/demethylation, andsingle nucleotide polymorphisms.

The method may further comprise comparing the sample protein expressionprofile to a control protein expression profile, wherein a differencebetween the sample protein expression profile and the control proteinexpression profile is indicative of the presence or absence, degree,severity, type or stage of osteoarthritis in the subject. The OAbiomarkers described herein are thus used in methods to detect thepresence of OA in a subject, to study populations of subjects as to theoccurrence of OA, and to evaluate OA treatment efficacy. Accordingly,the present disclosure provides methods for characterizing test samplesobtained from a subject suspected of having OA, for diagnosing OA in asubject, for identifying the subtype of OA, and for assessing theadvancement of OA in a subject. In such methods, the biomarkers'expression levels determined for a biological sample obtained from thesubject are compared to the levels in one or more control samples. Thecontrol samples may be obtained from a healthy subject (or a group ofhealthy subjects), from a subject (or group of subjects) with OA, from asubject (or group of subjects) with subtype I OA or subtype II OA,and/or from an subject (or group of subjects) with a specific stage ofthe disease (e.g., early OA or late OA). As mentioned above, the controlexpression levels of the biomarkers of interest are preferablydetermined from a significant number of individuals, and an average ormean is obtained. In certain preferred embodiments, the expressionlevels determined for the biological sample under investigation arecompared to at least one expression profile for OA, as described above.

The OA biomarkers having expression levels that correlate with thepresence or absence of OA, or OA degree, severity, type or stage, areattractive targets for the identification of new therapeutic agents(e.g., using screens to detect compounds or substances that inhibit orenhance the expression of these biomarkers). Accordingly, the presentdisclosure also provides methods for the identification of compounds orsubstances with the potential for effectively treating OA, or slowing OAprogression.

The OA biomarkers can be readily applied in various screening methods,for example for identifying a candidate substance as a therapeutic agentfor treating osteoarthritis. Such a method may comprise, for example, a)administering the candidate substance to a subject diagnosed withspontaneous osteoarthritis; b) measuring the expression level of two ormore OA polypeptides selected from the group consisting of MCP1, IL8,KC, MMP2, MMP3, IL6, MMP1, RANTES, MMP9, IL1B, Apolipoprotein A1,Apolipoprotein E, DCN, CILP and COMP in a biological sample from thesubject; and c) selecting the candidate substance as a candidatetherapeutic agent for treating osteoarthritis if the expression level ofeach of the two or more OA polypeptides in the biological sample islower than or equal to the expression level for the selected two or moreOA polypeptides in a biological sample from a control subject notadministered the test substance.

The methods may further include, for example, contacting a biologicalsystem that expresses at least one OA biomarker, with a candidate (test)substance for a time and under conditions sufficient for the candidatesubstance to change the expression of the at least one OA biomarker, andmeasuring a first OA biomarker expression level. The method may furthercomprise maintaining the biological system for the same time and underthe same conditions in the absence of the candidate substance, or aftercontacting the biological system with a control substance, thenmeasuring a second OA biomarker expression level; and comparing thefirst and second OA biomarker expression levels, wherein a first OAbiomarker expression level that is less than or greater than the secondOA biomarker expression level is indicative that the candidate substanceis a candidate therapeutic agent for treating OA. Any candidatesubstance or a plurality of substances (e.g. a library) can be screened,including but not limited to synthetic and natural substances, and anycombination of naturally occurring and synthetic substances. It shouldbe understood that such screening can be performed using multiple OAbiomarkers in parallel, which may be facilitated using any of manyreadily commercially available multiplex assays. The method may furtherinclude generating an OA expression profile for the one or more OAbiomarkers being evaluated, which can include for example expressioninformation for each OA biomarker under the test and control conditions.

Such screening methods may be carried out using any type of biologicalsystem, such as but not limited to a cell or cells, a biological fluid,a biological tissue, or an animal. Methods can be carried out using anysystem capable of showing cartilage degeneration in response to thepresence of induced or spontaneously occurring OA, including but notlimited to an animal model, a whole body part such as a knee, hip orelbow, or a portion thereof. Assay and screening methods can beperformed using cells grown in standard tissue culture. Preferably, suchcells are mammalian, and more preferably of canine or human origin.Cells may be primary cells, secondary cells, or immortalized cells andcan be prepared by techniques well known in the art, including cellsthat are genetically engineered to contain or knock out a selected gene,or are available from well known commercial sources such as the AmericanType Culture Collection, Manassas, Va. Those of routine skill in the artcan select a cell type or cell line according to generally recognizedprinciples such as the objective of the assay, type and number of OAmarker, drug being tested, and the like. Cells may be cultured usingstandard cell culture techniques, media and standards, such as growingand maintaining in a sterile environment at 37° C.

Any candidate substance identified by the screening methods can befurther tested in assays that allow for the determination of thecompound's properties in vivo. Suitable animal models of osteoarthritisare well known in the art, including models of spontaneously occurringOA and OA induced by surgical instability or genetic modification.Animal models of naturally occurring OA occur in knee joints of guineapigs, mice, and Syrian hamsters. Models of OA induced by surgicalinstability include medial meniscal tear in guinea pigs and rats, medialor lateral partial meniscectomy in rabbits, and medial partial or totalmeniscectomy or anterior cruciate transection in dogs. Transgenic mousemodels are known. Other animal models of OA that can be used forvalidating a candidate substance identified as a potential OAtherapeutic agents include many others described in detail in theliterature known to those in the art. Alternatively, the OA biomarkerscan be applied in a method for monitoring the effect of a treatment ofosteoarthritis in a subject. Such a method may comprise, for example, a)obtaining a first OA biomarker expression profile comprising measuringthe expression level of two or more OA polypeptides selected from thegroup consisting of MCP1, IL8, KC, MMP2, MMP3, IL6, MMP1, RANTES, MMP9,IL1B, Apolipoprotein A1, Apolipoprotein E, DCN, CILP and COMP in a firstbiological sample obtained from the subject before the osteoarthritistreatment is administered to the subject; b) obtaining a second OAbiomarker expression profile comprising measuring the expression levelof the two or more OA polypeptides selected in (a), in a secondbiological sample obtained from the subject after or while theosteoarthritis treatment is administered to the subject; and c)comparing the first OA biomarker expression profile with the second OAbiomarker expression profile, wherein if the expression level of each ofthe two or more selected OA polypeptides in the first OA biomarkerexpression profile is lower than or equal to the expression level forthe selected two or more OA polypeptides in the second biological samplefrom the subject is indicative of a therapeutic effect of theosteoarthritis treatment in the subject.

The terms “OA treatment” and “osteoarthritis treatment” as usedinterchangeably herein, refer to the application of, or administrationof any therapeutic device or agent that reduces the expression levels ina subject of any combination of two or more of the OA biomarkersdescribed therein, and/or that reduces or eliminates clinical symptomsof OA in a subject.

Once the responsiveness of a subject to a particular OA treatment hasbeen determined, an effective treatment may be selected for treating asubject with OA. If for example the OA is determined to be responsive toa particular pharmaceutical agent, then a treatment comprising the agentmay be given to the subject. If, however, the OA is determined to benon-responsive to the agent, then another treatment may be selected forthe subject. Thus, determining the responsiveness of a subject beforeadministering a treatment regime would spare subjects from potentiallytoxic or unhelpful treatments. Route of administration for any agentthat is a candidate substance for treating OA will vary depending uponfactors including the nature of the agent. The route of administrationmay be intradermal, transdermal, parenteral, intravenous, intramuscular,intranasal, subcutaneous, percutaneous, intratracheal, intraperitoneal,intratumoral, oral, perfusion, lavage, or direct injection. Thetreatment regimen can and will vary, depending on the type of OA, itslocation, its stage, and the health and age of the subject.

D. Reagents and Kits

Kits according to the present disclosure may comprise one or morereagents for measuring the expression of at least one OA marker, whereinchanges in the expression of the one or more OA in a subject relative toa control subject are indicative of the presence or absence, stage,severity or subtype of OA. OA markers comprise those listed in Table 1.A diagnostic kit may include at least one reagent that is capable ofspecifically binding to at least one OA marker as described herein, tothereby detect the expression level of one or more of the OA markers.

Each kit may comprise one or more specific binding reagents, eachbinding reagent specific to a selected OA marker or fragment thereof.The specific binding reagents may each comprise any molecule capable ofsuch specific binding, such as an antibody that specifically binds tothe protein marker, or fragment thereof, or a nucleic acid probecomplementary to a polynucleotide sequence such as a cDNA oroligonucleotide. By “specific binding” is meant the reaction of thereagent with the polypeptide to produce a detectable product, while notreacting detectably with other polypeptides having unrelated sequences.Specific binding reagents to be used in the measurement of theexpression of the OA markers can and will vary, depending upon the typeof technique to be used. For example, the kit may compriseoligonucleotide primers for QRT-PCR. Nucleic acid probes contained maybe included in a kit and are optionally provided together with a solidsubstrate, such as but not limited to beads, a chip, a plate, and amicroarray. Nucleic acid probes are optionally immobilized on thesurface of such a substrate. The kit may comprise fluorescent reporterprobes. The kit may also further comprise a reverse transcriptase, a Taqpolymerase, and appropriate buffers and salts.

A kit may comprise antibodies that can be used for an immunoassay, e.g.for an ELISA. The kit may further comprise a substrate for detection ofenzyme-conjugated antibodies. Antibodies that can be used in the methodsand included in kits include monoclonal and polyclonal antibodies,immunologically active fragments (e.g., Fab or (Fab) 2 fragments),antibody heavy chains, humanized antibodies, antibody light chains, andchimeric antibodies. Antibodies, including monoclonal and polyclonalantibodies, fragments and chimeras, may be prepared and purified usingmethods well known in the art, or obtained from scientific or commercialsources. Any binding agent can be directly or indirectly labeled with adetectable label.

Preferably, the detectable label generates a signal that can be measuredand is correlated, e.g. proportional to the amount of protein markerpresent in the sample being analyzed. Detectable labels, methods forlabeling molecules including polypeptides, antibodies andoligonucleotides are well-known in the art.

Additional reagents useful for analyzing biological samples, for exampledetermining the presence or absence, degree, severity, type or stage ofOA in a subject, may be provided in a kit. Depending on the technique orprocedure, the kit may further comprise one or more additional reagentssuch as, but not limited to, buffers such as extraction buffers,amplification buffers, hybridization buffers, immunodetection buffers,labeling buffers, or any equivalent reagent. Reagents may be supplied insolid (e.g., lyophilized) or liquid form, and these may optionally beprovided in individual packages using containers such as vials, packets,bottles and the like, for each individual reagent. Each component canfor example be provided in an amount appropriate for direct use or maybe provided in a reduced or concentrated form that can be reconstituted.Diagnostic and treatment monitoring kits can further comprise materialsand tools useful for carrying out diagnostic and monitoring methodsaccording to the present disclosure. The kits can be used for example indiagnostic laboratories, clinical or research settings. The kit mayfurther comprise instructions for use, including for example anyprocedural protocols and instructions for using the various reagents inthe kit for performing different steps of the process. Instructions forusing the kit according to one or more methods of the invention maycomprise instructions for processing the biological sample obtained fromthe subject and/or for performing the test, and instructions foranalyzing or interpreting the results. Instructions may be provided inprinted form or stored on any computer readable medium including but notlimited to DVDs, CDs, hard disk drives, magnetic tape and serverscapable of communicating over computer networks.

A kit may further comprise one or more control samples. A kit maycomprise at least one expression profile for OA, OA subtype, and/or OAprogression as described herein for use as comparison template.Preferably, the expression profile is provided as digital informationstored on a computer-readable medium.

It will be understood that generally, components of a kit areconveniently packaged or bound together for ease of handling incommercial distribution and sale.

E. Adaptations of the Methods of the Present Disclosure

By way of example, and not of limitation, examples of the presentdisclosures shall now be given.

Example 1 Assessment of Proteins in Media from In Vitro Cultured Normaland OA Articular Cartilage Explants

Articular cartilage was harvested from the femoral head of dogs (n=6)undergoing total hip replacement due to chronic OA and from dogs (n=6)with no overt clinical signs of OA and euthanized for reasons unrelatedto the present study. Two 4 mm explants were created from the tissue ofeach animal and incubated in 500 ul of DMEM with supplemental nutrientsfor 7 days. Culture media from each individual was analyzed using acanine cytokine and chemokine immunoassay for MCP1, IL-8 and KC(Millipore) based on the xMAP platform. A second aliquot was analyzedusing a multiplex human MMP immunoassay for MMPs 2, 3 and 13 (R&DSystems) that has been shown to cross react with canine samples.Clinically relevant subgroups were then created based on OA-status andthe media from each subgroup was pooled for proteomics analysis. Eachmedia pool was acetone precipitated and quantified to ensure equivalentprotein loading for one-dimensional polyacrylamide gel electrophoresis(1D-PAGE) with reducing conditions. Gel separation of the normal groupcould not be pursued due to insufficient volume and very low proteinconcentration of the normal culture media. Following gel separation ofthe remaining pooled samples, each lane was cut into 8 equal sections(total n=24) and in-gel trypsin digests were performed. Each digest wasanalyzed by LC-MS/MS using LTQ Orbitrap instrumentation. Results werestatistically evaluated with the unpaired t-test with significance setat p<0.05. Following initial analysis, high abundance blood proteinswere “hidden” from the instrument and re-analysis of the subclinical OAand clinical OA was performed. Fold changes between these two groupswere determined using the Scaffold 2 Viewer Proteome software.

Subclinical OA versus Clinical OA (mild and severe): Alterations of 57proteins were identified in media between subclinical OA and clinical OAgroups, including numerous high abundance blood proteins (serum albumin)and several extracellular matrix (ECM) proteins. Cartilage OligomericMatrix Protein (COMP) was significantly higher in the subclinical OAgroup compared to clinical OA groups (p=0.0033).

Subclinical OA versus Severe Clinical OA (FIG. 1): The bar graphs showquantitative values obtained by Mass-Spec for select proteins fromsubclinical OA and clinical OA (high) groups following the removal ofhigh abundance blood proteins. Alterations of 155 proteins wereidentified in media between subclinical OA and severe clinical OA groupsonce high abundance proteins were masked. Cartilage Intermediate LayerProtein (CILP), Decorin and COMP were all lower in the severe clinicalOA group [4.2×, 4.0× and 1.4× respectively] (FIG. 1A). ApolipoproteinsA1 and E were 9.1× and 2.6× higher in the severe clinical OA group,respectively (FIG. 1B).

Removal of high abundance proteins, such as albumin, greatly increasedthe detection of lower abundance proteins in this study. COMP iscurrently one of the most studied biomarkers in joint disease, and ithas been shown to be significantly increased during the initial stagesof OA followed by a decline in the later stages of disease. COMP washigher in the dogs in the subclinical OA group in this study, thusproviding additional support for the use of this novel biomarker panelfor the diagnosis of early OA. Another protein of interest isApolipoprotein A1 (ApoA1). ApoA1 has been shown to be higher inosteoarthritic canine and human synovial fluid and human articularcartilage compared to normal, but to our knowledge we are the first toconfirm the release of ApoA1 from canine articular cartilage. Theseresults provide continued support for the use of canine tissues intranslational research for human OA, and additional support for the useof a biomarker panel for diagnosis and staging of early OA.

Further study was undertaken to: 1) delineate the alterations ofcytokine and chemokine concentrations in synovial fluid inosteoarthritic and non-osteoarthritic knee joints and 2) determine ifany cytokine and chemokine fluctuations discern OA using receiveroperating characteristic (ROC) curve analysis. Twenty-one adult, intactfemale, hound dogs >20 kg were included in this study. Each dogunderwent one of four arthroscopic procedures: transection of theanterior cruciate ligament (ACL-T), transection of the meniscus (MR),creation of two full-thickness grooves in the cartilage of the medialfemoral condyle (Groove) or probe manipulation of all joint landmarkswithout insult (SHAM). The non-operated, contralateral hind limb servedas an internal control for each dog. Synovial fluid was collectedimmediately prior to surgery on the operated limb, and 12 weekspost-operatively from both the operated and contralateral control limbs.These were analyzed using a multiplex canine cytokine and chemokineimmunoassay (Millipore) for IL-2, IL-4, IL-7, IL-8, IL-15, IL-18, IP-10,INF-γ, TNF-α, MCP1, KC, and GM-CSF based on the xMAP platform. Resultswere statistically evaluated with the unpaired t-test or theMann-Whitney Rank Sum test with significance set at p<0.05. Imagingstudies (including ultrasound and magnetic resonance imaging),arthroscopy and histopathologic data were also collected to fullycharacterize the pathology of all joint tissues.

In the synovial fluid, monocyte chemoattractant protein 1 (MCP1) wassignificantly increased in ACL-T joints (n=5) 12 weeks after surgerycompared to day 0 (n=21; p<0.001) and the SHAM joints at 12 weeks (n=5;p<0.009). Increased MCP1 was also observed in the Groove (n=6) and MRgroups (n=5) at 12 weeks compared to day 0, but statistical significancewas not reached. Interleukin-8 (IL-8) was significantly increased at 12weeks in the ACL-T and MR dogs compared to day 0 (n=21; A: p=0.001, M:p=0.018), the non-operated limb at 12 weeks (n=21; A: p=0.002, M:p=0.018), and the SHAM group (n=3; A: p=0.019, M: p=0.049) at 12 weeks.Keratinocyte-derived chemoattractant (KC) was significantly decreased inthe Groove group at 12 weeks (n=6) compared to day 0 (n=21; p=0.009).The remaining cytokines and chemokines were below detectable levels inthe synovial fluid of these animals. Using receiver operatingcharacteristic curves, areas under the curve (AUC) were calculated forIL-8, MCP1 and KC individually and as a combined panel (Table 2).

TABLE 2 Areas under the curve (AUC) ± SE for IL-8, KC or MCP1 ACL-TvsSHAM OA vs SHAM IL-8 1 0.86 ± 0.07 MCP1 0.67 ± 0.17 0.59 ± 0.17 KC 0.74± 0.17 0.62 ± 0.17 Combined 0.88 ± .11 

Thus in canine models of OA, changes in cytokine and chemokine levelsoccur within the synovial fluid after OA induction. ROC curves fordiagnostic tests with perfect discrimination between normal and OA havean AUC=1.0. The results demonstrated that a biomarker panel includingmonocyte chemoattractant protein 1 (MCP1/CCL2), interleukin-8(IL-8/CXCL8) and keratinocyte-derived chemoattractant (KC/CXCL1)demonstrates strong discriminatory ability for distinguishing OA dogsfrom normal dogs.

Example 2 Assessment of Synovial Fluid and Serum Cytokines, Chemokinesand Matrix Metalloproteinases (MMPs) in Dogs with SpontaneouslyOccurring OA

Methods: Informed client consent was obtained for each dog included inthis study. Blood and synovial fluid were obtained from 10 adult mediumand large breed dogs presenting to the UMC-VMTH for surgicalintervention of unilateral stifle (knee) OA (Pre-Op OA; n=10). Thesedogs ranged from 3-8 years old (mean 5.15 years median might be better).Synovial fluid was obtained from the affected stifle via routine asepticarthrocentesis, and blood was collected via jugular venipuncture.Clinical knee OA was confirmed in each dog by a board-certifiedveterinary orthopedic surgeon. Radiographic evidence of OA was confirmedby a board-certified veterinary radiologist. All dogs underwent kneesurgery for cruciate ligament deficiency and recovered uneventfully.Eight to 12 weeks later, the dogs returned for a postoperative re-check,and blood and synovial fluid were collected again to assess changes inmarkers after surgical intervention. The control group was comprised ofnine medium and large breed adult dogs ranging from 2-5 years old (mean2.9 years). These dogs had no clinical history of joint trauma, were notlame and were deemed to be free of clinical OA by a board certifiedveterinary orthopedic surgeon. Radiographic evaluation of the shoulders,knees and hips verified the absence of OA. Blood and synovial fluid werecollected in a similar manner to the OA dogs at a time convenient to theclients. The synovial fluid samples were analyzed in duplicate using amultiplex canine cytokine and chemokine immunoassay (Millipore Corp. St.Louis, Mo., USA) based on the xMAP platform (Qiagen Inc.) for IL-2,IL-4, IL-6, IL-7, IL-8, IL-10, IL-15, IL-18, IP-10, INF-γ, TNF-α, MCP1,KC, and GM-CSF per manufacturers' instructions. Another 25 μls wasanalyzed in duplicate using a multiplex human matrix metalloproteinase(MMP) immunoassay (R&D Systems, Minneapolis, Minn., USA) based on thexMAP platform (Qiagen, Inc.) for MMP1, MMP2, MMP3, MMP9 and MMP13. Thisassay has been previously shown by our laboratory to cross-react withsamples of canine origin. Results were statistically evaluated with anunpaired t-test or Mann-Whitney Rank Sum test (SigmaStat 3.5; SystatSoftware, Incorporated, San Jose, Calif., USA) with significance set atp<0.05. Results: Results obtained following the methods described aboveare summarized in FIGS. 2A and 2B and Table 3 (below).

TABLE 3 Proteins exhibiting differences in expression between synovialfluid collected from normal and OA canine knees SYNOVIAL FLUID FOLDCHANGE Identified Protein Normal: OA Aggrecan core protein 2.08CIusterin 0.3 Alpha-2-macroglobulin 0.22 Angiotensinogen 0.41Apolipoprotein B-100 0.13 Complement C3 0.4 Complement factor J 0.43Fibronectin 1 isoform 1 preproprotein 0.32 Transthyretin 3.25Zinc-alpha-2-glycoprotein 0.21

In synovial fluid, IL8 and KC were significantly higher in the Pre-Op OAdogs compared to normal dogs (p<0.001; p=0.01) and in the Post-Op OAdogs compared to normal dogs (p=0.002; p=0.03). Both analytes were lowerin Post-Op OA dogs compared to Pre-Op OA dogs, but this decrease was notstatistically significant. MCP-1 was significantly higher in the Pre-OpOA dogs and Post-Op OA dogs compared to normal dogs (p<0.001; P=0.009),and there was a significant decrease in MCP-1 following surgery comparedto pre-surgery values (p=0.01). IL8 was significantly higher in thePre-Op OA dogs compared to normal dogs (p=0.02), but the remainingcytokines and chemokines were below the limit of detection. MMP2 washighest in the Post-Op OA dogs, and this was significantly higher thanthe normal dogs (p=0.010). MMP3 was highest in the Pre-Op OA dogs andlowest in the Post-Op OA dogs, but these changes did not reachstatistical significance. (FIGS. 2A and 2B). The performances of thesemarkers as individuals and as a combined panel were evaluated throughROC curve analysis using statistical software (SAS Institute).Specifically, ROC curves were generated using JMP 7.0.2 software (SASInstitute) and used to determine the discriminatory abilities of thevarious biomarker combinations. Several biomarker panels led to perfectdiscrimination (AUC=1.0) between groups (Table 4). In Table 4, “CytoMarkers” are IL8, MCP1 and KC, and “Cyto and MMP” refers to IL8, MCP1,KC, MMP2 and MMP3.

TABLE 4 Analyte panels that lead to perfect AUCs Area Under the CurvesComparison Cyto markers Cyto and MMP Normal vs Pre-surgical OA 1 1Normal vs Post-surgical OA 1 1 Pre-surgical vs Post-surgical OA 1 Normalvs OA 1

The remaining serum and SF were separated with 1D-PAGE and analyzed byliquid chromatography mass spectrometry (LC-MS/MS). Matches weresearched against the National Center for Biotechnology Information(NCBI) non-redundant database taxonomy-limited to dogs only. Significantdifferences between groups were represented by a p<0.05 and a foldchange >2.0.

In serum, MMP2 and MMP3 were highest in the normal dogs and lowest inthe Pre-Op OA dogs. MMP2 was significantly higher in normal dogs andPost-Op OA dogs compared to Pre-Op OA dogs (p=0.003; p=0.03), but therewas not a significant difference between normal and Post-Op OA dogs.MMP3 was significantly higher in normal dogs and Post-Op OA dogscompared to Pre-Op OA dogs (p=0.002, p=0.03), but there was not asignificant difference between Pre-Op and Post-Op OA dogs. Significantdifferences were not detected between groups for IL8, KC, MCP1, IL18,IL2, IL7 or GMCSF, and the remaining analytes were below the limit ofdetection for the assay.

Thus, ROC curve analysis demonstrates for the first time that abiomarker panel measuring synovial fluid MCP1, IL8, KC, MMP2 and MMP3has the ability to consistently differentiate normal healthy knees fromknees in dogs with spontaneously occurring clinical OA. In addition,MCP1 was significantly lower in the Post-Op OA dogs compared to theirPre-Op OA values, and IL8 and KC declined after treatment as well,indicating that this novel biomarker panel has great potential forclinical use in both diagnostic and treatment monitoring applications.The three cytokines were able to repeatedly distinguish between Pre-OpOA and Post-Op OA individuals (AUC=0.9) when they were measured in thesynovial fluid, but the addition of MMP2 and MMP3 to the panel improvedthe performance (AUC=1.0), indicating that the addition of MMPs to thisor any diagnostic biomarker panel would be useful for treatmentmonitoring or prognosis. Thus the results show that use of synovialfluid biomarkers has important clinical application based on therelative ease in obtaining samples, the associated costs, and the jointspecific nature of these evaluations. Addition of MMPs to the biomarkerpanel enhances its capabilities, especially with respect to treatmentmonitoring.

Example 3 OA Biomarkers in Synovial Fluid of Human Patients

OA biomarkers in the synovial fluid of human patients were investigated.Specific goals were 1) to identify and measure the concentration ofspecific MMPs and inflammatory cytokines released to the synovial fluidof normal and OA patients undergoing total knee arthroplasty; and 2) tocorrelate the production of these inflammatory biomarkers withradiographic severity of disease. All procedures were performed with IRB(IRB#1042248) approval. Synovial fluid was aspirated from three “truenormal” patients (23, 27, 28 y/o) with no previous knee injury, clinicalsymptoms of knee pain or OA, or operative procedures performed. Synovialfluid was aspirated from 18 patients (21 knees) with OA immediatelypreceding their total knee arthroplasty

procedure (age range=44-86 y/o). Equal volumes of hyaluronidase treatedsynovial fluid samples were analyzed using the Fluorokine MAP human MMP(MMP-1, -2, -9, and 013) and cytokine (Interleukin lf3 (IL-lf3), IL-6,IL-8, Tumor necrosis factor-α (TNF-α), Macrophage inflammatory protein1α (MIP-1α), MIP-1f3, Monocyte chemotactic protein 1 (MCP-1), RANTES)multiplex panels (R&D Systems). A log transformation was performed tonormalize the data for statistical analysis. Results from the normal andOA groups were evaluated using an unpaired t-test and between analytesusing a Pearson product moment correlation. Significance was set atp<0.05. Each patient eventually undergoing TKA had a standing APradiograph performed during the pre-operative evaluation. The ModifiedKellgren and Lawrence scoring system was applied to both the medial andlateral compartments and then totaled. The radiographic scores werecorrelated with the log transformed MMP/cytokine data using Spearmanrank order correlation with significance set at p<0.05.

Normal vs. OA: Of the 12 biomarkers tested, MMP-1, IL-6, IL-8, andRANTES were significantly higher in the synovial fluid of OA patientscompared to normal patients, as shown in FIG. 3. Three of the twelvewere trending toward significance: MIP-1f3, MCP-1, and MMP-2 (notrepresented in FIG. 3, p=0.105). MMP-9, MMP-13, IL-lf3, TNF-α, andMIP-1α were below the detection limits of this assay for all patients.

Correlation between Analytes: MMP-1 had a moderate positive correlationwith MMP-2 (r=0.43), IL-6 (r=0.52), IL-8 (r=0.43), and RANTES (0.58).IL-6 had a strong (r=0.79) positive correlation with IL-8 and a moderate(r=0.44) positive correlation with MMP-2. MCP-1 had a moderate (r=0.56)positive correlation with IL-6 and strong (r=0.70) positive correlationwith IL-8.

Correlation with Radiographic Scoring: The radiographic scoring systemhad strong positive correlations with IL-6 (r=0.71) and IL-8 (r=0.82),and moderate positive correlations with MMP-1 (r=0.353) and MCP-1(r=0.483).

It is believed this data provides for the first time an indication ofsynovial fluid biomarkers for OA in human patients. Importantly, truenormal controls were used for this study, which is not often the caseand thus a major limiting factor in human clinical studies. The resultsfrom this study suggest that IL-6 and IL-8 are particularly intriguingas potential biomarkers as a significant increase in these two cytokineswas shown in OA patients, and also a strong correlation between the two,and strong correlations to severity of radiographic change. Also shownwas a moderately strong correlation noted between severity ofradiographic change and MMP-1 and MCP-1 levels. The correlations toradiographic severity are particularly important as it provides animmediate clinical relevance to the investigation of these proteins asOA biomarkers. IL-6, IL-8, MMP-1, and MCP-1 can readily be assessed as apanel in small volume samples of synovial fluid using a commerciallyavailable assay.

The results from this Example together with the results of Examples 1and 2 show that IL-6, IL-8, MMPs, KC, and MCP-1 provide a biomarkerpanel for both presence and severity of disease and treatment monitoringin both canine and human patients.

Example 4 Validation of Novel OA Biomarker Panels for Distinguishing andDetermining the Severity of Various Forms of Arthritis in Dogs

Further study can be used to validate the novel OA biomarker panels fordistinguishing and determining the severity of various forms ofarthritis in dogs. A starting hypothesis is that the novel OA biomarkerpanel can have high sensitivity and specificity (>0.9) and ROC data(>0.8) for determining the presence and severity of OA in clinicalcohorts of canine patients. To validate a novel OA biomarker panel fordiagnosis and disease staging in clinical canine patients, synovialfluid, urine, and blood is collected via routine arthrocentesis,cystocentesis, and jugular venipuncture, respectively, from dogs (n=20per group minimum) with normal stifles (knees), stifles affected byinfectious arthritis, stifles affected by a developmental disorder(patellar luxation), and stifles affected by a degenerative disorder(cruciate ligament disease) upon presentation to our Veterinary MedicalTeaching Hospital (VMTH). The University of Missouri's VMTH admits wellover 100 cases in each of these cohorts each year. Epidemiologic data isobtained and recorded in the medical record for each case.

Clinical Assessments—Clinical lameness scores are determined and scoresassigned in blinded fashion by two veterinary orthopedic surgeons basedon visual examination of gait using an established scoring system (10).Comfortable range of motion (CROM) in each stifle is determined byplacing a goniometer on each limb such that one arm of the goniometer isaligned with the femur and one arm is aligned with the tibia with therotation point centered at the joint line. Each stifle is flexed andextended to the point allowable without definitive resistance or signsof pain from the dog. The maximal flexion and extension angles isrecorded. This procedure is repeated 3 times. The CROM is determined bysubtracting the mean flexion angle from the mean extension angle foreach stifle.

Radiographic Assessment—The dogs are sedated to obtain craniocaudal andmediolateral digital radiographic views of affected stifles. Theradiographs are scored by one investigator blinded to informationregarding patient cohort and clinical signs, utilizing a subjectivescoring system. (13, 31). For this scoring methodology, nine regions ofthe stifle are evaluated and given a score from 0-3 based on severity ofsecondary radiographic changes associated with clinical OA in dogs.Therefore, each stifle receives a score ranging from 0-27. Stiflesscored from 0 to 4 are considered normal. Stifles scored from 5 to 9 areconsidered to have mild OA.

Stifles scored from 10-18 are considered to have moderate OA, andstifles scored 19-27 are considered to have severe OA.

Arthroscopic Assessment—Arthroscopic evaluation of affected stifles areperformed using craniolateral and craniomedial portals. All articularsurfaces of the patella, femur and tibia are examined and scored withrespect to degree of articular cartilage damage (ICRS system). Meniscal,ligamentous, and synovial pathology are arthroscopically assessed anddescribed in terms of nature, extent, and location. Dogs in the normalstifle group do not undergo arthroscopy.

Biomarkers—A small aliquot (25 μl) from each sample is thawed. For urineand synovial fluid, samples are centrifuged at 14,000 rpm for 10 minutesto pellet debris, and the supernatant removed. Synovial fluid samplesare incubated with hyaluronidase (MP Biomedicals, LLC, Solon, Ohio) at37° C. for 60 minutes to decrease viscosity. Each aliquot of synovialfluid, urine, and serum is analyzed in duplicate using multipleximmunoassays based on the xMAP platform (Qiagen Inc., Valencia, Calif.)for IL-lf3, IL-2, IL-4, IL-6, IL-7, IL-8, IL-10, IL-15, IL-18, IP-10, 15INF-γ, TNF-α, MCP1, KC, GM-CSF, COMP, Apo1, Apo2, MIP-1α), MIP-1f3 MMP1,MMP2, MMP3, MMP9 and MMP13 according to the manufacturers' directions.Briefly, each of the samples is admixed with monoclonalantibody-charged, small (5.6 micron), polystyrene microspheres in a96-well plate. Following an overnight incubation at 4° C., a polyclonalsecondary antibody is added, as well as streptavidin-phycoerythrin. Themedian fluorescence intensity (MFI) is determined for each sample, andconcentrations (pg/ml) obtained from a standard curve.

Statistical Analyses—Strength of correlations between each biomarker andcombinations of biomarkers to detect presence and stage of disease isanalyzed using a Pearson's Correlation. Sensitivity, specificity, andreceiver operating characteristic curve (ROC) data is calculated foreach biomarker and combinations of biomarkers to determinediscriminatory potential between presence, type, and severity of diseasefor the various cohorts based on all outcome measures employed.

Example 5 Validation of Novel OA Biomarker Panels for Distinguishing andDetermining the Severity of Various Forms of Arthritis in Humans

Further study can also be used to validate the novel OA biomarker panelsfor diagnosis and disease staging in clinical human patients. Withinformed patient consent under IRB approval, synovial fluid, urine, andblood is collected via routine arthrocentesis, free catch urinecollection, and peripheral venipuncture, respectively, from patients(n=20 per group minimum) with normal knees, knees with rheumatoidarthritis, knees with meniscal tears and grade 1-2 articular cartilagepathology, knees with post-traumatic OA, and knees with end stage OAundergoing total knee arthroplasty at The University of MissouriHospitals and Clinics (UMHC).

The UMHC admits well over 200 cases in each of these cohorts each year.Epidemiologic data is obtained and recorded in the medical record foreach case.

Clinical Assessments—Knee examination is performed on all participantsand findings recorded. The 36-Item Short-Form Health Survey (SF-36) isused to assess the patient quality of life. 2 This is a self-reportedmultidomain questionnaire, reflecting the patient's pain, strength, andaffect secondary to their disease. Functional outcome measures isassessed via the Western Ontario McMaster Universities OsteoarthritisIndex (WOMAC)(34).

Radiographic Assessment—Knee radiographs are assessed using the ModifiedKellgren-Lawrence scoring system (21) where the medial and lateralcompartments is reviewed, scored for the severity of changes and thenscores totaled.

Whole-joint Surgical Assessment—At the time of surgery (arthrotomy orarthroscopy), all articular surfaces of the patella, femur and tibia areexamined and scored with respect to degree of articular cartilage damage(ICRS system). Meniscal, ligamentous, and synovial pathology areassessed and described in terms of nature, extent, and location.Patients in the normal group do not undergo surgical assessment.

Biomarkers—A small aliquot (25 μl) from each sample is thawed. For urineand synovial fluid, samples are centrifuged at 14,000 rpm for 10 minutesto pellet debris, and the supernatant removed. Synovial fluid samplesare incubated with hyaluronidase (MP Biomedicals, LLC, Solon, Ohio) at37° C. for 60 minutes to decrease viscosity. Each aliquot of synovialfluid, urine, and serum is analyzed in duplicate using multipleximmunoassays based on the xMAP platform (Qiagen Inc., Valencia, Calif.)for IL-lf3, IL-2, IL-4, IL-6, IL-7, IL-8, IL-10, IL-15, IL-18, IP-10,INF-γ, TNF-α, MCP1, KC, GM-CSF, COMP, Apo1, Apo2, MIP-1a), MIP-1f3 MMP1,MMP2, MMP3, MMP9 and MMP13 according to the manufacturers' directions.Briefly, each of the samples is admixed with monoclonalantibody-charged, small (5.6 micron), polystyrene microspheres in a96-well plate. Following an overnight incubation at 4° C., a polyclonalsecondary antibody is added, as well as streptavidin-phycoerythrin. Themedian fluorescence intensity (MFI) is determined for each sample, andconcentrations (pg/ml) obtained from a standard curve.

Statistical Analyses—Strength of correlations between each biomarker andcombinations of biomarkers to detect presence and stage of disease isanalyzed using a Pearson's Correlation. Sensitivity, specificity, andreceiver operating characteristic curve (ROC) data is calculated foreach biomarker and combinations of biomarkers to determinediscriminatory potential between presence, type, and severity of diseasefor the various cohorts based on all outcome measures employed.

The present disclosure illustratively described herein suitably may bepracticed in the absence of any element or elements, limitation orlimitations which are not specifically disclosed herein. Thus, forexample, in each instance herein any of the terms “comprising,”“consisting essentially of” and “consisting of” may be replaced witheither of the other two terms. The terms and expressions which have beenemployed are used as terms of description and not of limitation, andthere is no intention that in the use of such terms and expressions ofexcluding any equivalents of the features shown and described orportions thereof, but it is recognized that various modifications arepossible within the scope of the present disclosure claimed. Thus, itshould be understood that although the present disclosure has beenspecifically disclosed by preferred embodiments and optional features,modification and variation of the concepts herein disclosed may beresorted to by those skilled in the art, and that such modifications andvariations are considered to be within the scope of this invention asdefined by the appended claims.

All patents and publications mentioned in the specification areindicative of the levels of those skilled in the art to which thepresent disclosure pertains. All patents and publications are hereinincorporated by reference to the same extent as if each individualpublication was specifically and individually indicated to beincorporated by reference.

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What is claimed is:
 1. A method to detect osteoarthritis in a humansubject comprising: (a) using a protein detection method to determinethe levels of three or more different osteoarthritis marker polypeptidesin a synovial fluid sample collected from a first human subject, whereinthe three or more different osteoarthritis marker polypeptides compriseMCP1, IL8, and KC; (b) using the protein detection method to determinethe levels of three or more different osteoarthritis marker polypeptidesin a biological fluid sample collected from a second human controlsubject, wherein the three or more different osteoarthritis markerpolypeptides comprise MCP1, IL8, and KC; (c) using the level of each ofthe three or more different osteoarthritis marker polypeptides in thefirst human subject and the second human control subject to calculate aprobability of the presence of osteoarthritis in the first humansubject, and determining whether the probability is greater than orequal to at least about 80%; and (d) when the probability from step (c)is greater than or equal to at least about 80%, determining thatosteoarthritis is present in the first human subject.
 2. The method ofclaim 1, wherein the level of expression of at least one additionalosteoarthritis marker polypeptide is measured.
 3. The method of claim 2,wherein the at least one additional osteoarthritis marker polypeptide isselected from the group consisting of MMP2 and MMP3.
 4. The method ofclaim 2, comprising measuring in the biological fluid samples from thehuman test and control subjects the level of expression of MCP1, IL8,KC, MMP2 and MMP3.
 5. The method of claim 4, further comprisingmeasuring in the biological fluid samples from the human test andcontrol subjects the level of expression of at least one additionalosteoarthritis marker selected from Apolipoprotein A1 and ApolipoproteinE.
 6. The method of claim 5, wherein the level of expression of at leastseven different osteoarthritis marker polypeptides is measured, whereinthe selected osteoarthritis marker polypeptides comprise MCP-1, IL8, KC,MMP2, MMP3, Apolipoprotein A1 and Apolipoprotein E.
 7. The method ofclaim 1, wherein the first human subject is at risk of havingosteoarthritis.
 8. The method according to claim 1, wherein the proteindetection method is selected from the group consisting of: LUMINEX,ELISA, immunoassay, mass spectrometry, high performance liquidchromatography, two-dimensional electrophoresis, Western blotting,protein microarray, and antibody microarray.
 9. The method of claim 8,wherein the protein detection method is an immunoassay.
 10. The methodof claim 1, wherein the probability is calculated in a method comprisingthe steps of: determining the levels of three or more biomarkers in thefirst subject and the second subject, generating a receiver operatingcharacteristic (ROC) curve, and calculating the area under the ROC curve(AUC), the area under the curve (AUC) providing the probability of thepresence of osteoarthritis in the first subject.
 11. The method of claim1, wherein the second human control subject is a true normal controlsubject.
 12. A method to detect osteoarthritis in a human subjectcomprising: (a) using a protein detection method to determine the levelsof three or more different osteoarthritis marker polypeptides in asynovial fluid sample collected from a first human subject, wherein thethree or more different osteoarthritis marker polypeptides compriseMCP1, IL8, and KC; (b) using the protein detection method to determinethe levels of three or more different osteoarthritis marker polypeptidesin a biological fluid sample collected from a second human controlsubject, wherein the control subject is a true normal control, andwherein the three or more different osteoarthritis marker polypeptidescomprise MCP1, IL8, and KC; (c) using the level of each of the three ormore different osteoarthritis marker polypeptides in the first humansubject and the second human control subject to calculate a probabilityof the presence of osteoarthritis in the first human subject, anddetermining whether the probability is greater than or equal to at leastabout 80%; and (d) when the probability from step (c) is greater than orequal to at least about 80%, determining that osteoarthritis is presentin the first human subject.